to work on:

Pacific Giant Salamander Image Source: Gary Nafis1

Introduction

(! this syntax is SoOoO STALE, HALP ! (but the info is good))

Pacific Giant Salamanders,(Dicamptodon tenebrosus) are the largest terrestrial salamander in North America, growing up to 13 inches in total length 2. Pacific Giant Salamanders(PGS) populations range from northern California to the Canadian border, but are absent from the Olympic Peninsula. Thier habitats consist of wetlands such as permanent rivers, streams, creeks and pools of forests3. PGS populations may be affected by increases in pressures associated with logging such as habitat destruction and increased silt in the water due to upstream disturbances. This report analyses the differences in PGS populations between old growth(OG) forests and clear cut (CC) forests located in the H.J. Andrews Experimental Forest near Blue River, Oregon.

Map Source: Oregon State University4

Data and Methods

The data5 analyzed for this report was collected from Mack Creek in the H.J. Andrews Experimental Forest in Oregon. Cuttthroat trout (Onchorhyncus clarki clarki) populations have been monitored since 1987 then monitoring of Pacific Giant Salamanders began in 1993. H.J. Andrews Experimental Forest contains two sections of clearcut forest (cleared in 1963) and an upstream 500 year old coniferous forest5. These two sections will be referred to as “clear cut”(CC) and “old growth”(OG) throughout this report.

Specimen were sampled via electro-fishing and captured vertebrates were measured and weighed. This report uses the salamander data regarding section (old growth or clearcut), channel-specification (cascades, pool or side-channel), salamander weight (grams), and the total salamander counts observed(n).

Salamander abundance across locations was explored using statistical tests including a chi-squared test, two-sample t-test, Cohen’s d, Levene’s test, one-way ANOVA, and Tukey’s test.

Results

Results A:

Describe the trends in graph (in text).

Figure 1 shows the overall trend of PGS population counts being lower in clear-cut ares when compared to counts from old-growth forest. The annual change, growth or declines, of the two populations follows the same trend. Between the years 2011 and 2014 there was an obvious decline in population of both sections. This decline in population may be due to….

Results B:

Pacific giant salamander observations from 2017 were [compiled] to evaluate salamander counts and proportions in different channel classifications (pool, cascade, or side-channel) within Mack Creek for the two sections (old growth and clear cut).

Talbe 1 [indicates] that the majority of salamanders observed in both clear cut and old growth forest sections were found in cascades (over 60% for both). Side channels [contained] the [second most] observatoins (between 23-24% of observations). The [lowest] proportion of salamanders were observed in pools (less than 15% of relative abundance). Overall, more salamanders were observed in clear cut than old growth sections–368 and 320 respectively.

Table 1 [displays] the 2017 salamander counts in each section and the relative proportions of salamanders in each channel classification(cascade, pool or side-channel)
Section Cascades Pool Side-channel
Clear cut 247 (67%) 31 (8%) 90 (24%)
Old growth 201 (63%) 45 (14%) 74 (23%)

Results C:

A chi-square test was used to determine if there is an association between forest secction (clear cut or old growth) and channel classification (cascades, pool, or side channel). The results indicate that forest section does not have a significatn effect on salamander location, and are thus independnet of each other (\(\chi\)2(2) = 5.54, p = 0.06).

Results D:

Pacific giant salamander observations in 2017 within clear cut and old growth forest sections have similar counts and distributions of salamander weight. The two sections of forest in 2017 have overall salamander counts that differ by only 40 individual specimen. Therefore, it is important to compare statistics on salamander weight to find potential differences between the two sample populations.

PGS mean weight is 1.08 grams greater in clear cut sections than in old growth (7.78g and 6.7g, respectively). The results indicate that there is not a significant difference in mean weights for Pacific giant salamanders observed in the two forest sections (t(683.21) = (1.49, p = (0.138).

Large sample size, a lack of significance difference between sample means, and a small effect size (Cohen’s d = 0.11) indicates a lack of association between PGS weight and forest condition.

Results E: PGS weights within different channel classifications

Compare weights of Pacific giant salamanders in pools, cascades and side-channels of Mack Creek in 2017. Pool salamander observations from both the old growth and clear cut sections for this part (i.e., you will not consider “section” as a factor here).

Second, answer: Is there a significant difference in mean weights for Pacific giant salamanders observed in pools vs. cascades vs. side-channels in 2017? Describe the results of your statistical analysis in text, within the context of broader (and more important) measures of differences between groups (some options: means differences, effect sizes, percent differences, etc).

unittype mean_weight sd_weight sample_size se_weight var_weight
C 7.520850 9.027747 448 0.4265209 81.50021
P 9.297500 13.622957 76 1.5626603 185.58494
SC 5.676646 8.265256 164 0.6454081 68.31446

Mean weights and sample size for PGS observations drawn from [different] channel classifications differ slightly. In cascades, 448 salamanders with a mean weight of 7.52g were [observed]. Pools [observed] a mean weight of 9.3g among a sample of 76 salamanders. And the 164 salamanders observed in side channels were found to have a mean weight of 5.68g.

[Overall, counts differed by a range of 372 salamanders, while average weights differed by a range 3.62g.]

Variance in weight among channel classifications are somewhat similar. The channel with the largest variance is less than 4x greater than that of the channel with the smallest variance. A Levene’s Test shows that variances are equal (because p-val >0.05). Therefore, it is appropriate to execute a one-way ANOVA to compare means between the three groups.

A one-way ANOVA indicates that the mean weights for the 3 classifications are NOT the same insert in-text shindigaroo. In response, a post-hoc pairwise comparison using Tukey is [used] to test which of the 3 channel classifications differ from eachother (based on mean weight values).

A one-way ANOVA, paired with post-hoc tukey’s HSD, reveals a significant difference only in mean salamander wieght between salamanders found in side channels and pools insert tukey values for sc-p. Cascades did not differ significantly from pools or side channels (insert tukey values for P-C and SC-C, respectively).

MUST TALK ABOUT EFFECT SIZE OR SOMETHING THAT MAKES THESE DIFFERENT

  • We could do effect size for each combo? that might be interesting and tell us something

Third, describe any concerns you have about comparing means across the groups. What might be another option to consider moving forward with the analysis? (You don’t need to actually do that here, just describe briefly in 1-2 sentences.) - Using means to compare groupd lead to skewed data, as seen in Figure 2, there were many outliers in the weights of salamanders within each channel section. For data that contains outliers, comparing medians elimanates the skew and allows for more [equal, levelized, ] comparison among groups.

References

  1. “Dicamptodon tenebrosus; Pacific Giant Salamander.” Gary Nafis, California Herps, http://www.californiaherps.com/salamanders/images/dtenebrosusfchu3086.jpg

  2. “Coastal Giant Salamander - Dicamptodon tenebrosus.” California Herps, 2019, http://www.californiaherps.com/salamanders/pages/d.tenebrosus.html

  3. “Coastal Giant Salamander - Dicamptodon tenebrosus.” IUCN Red List of Threatened Species, 2015, https://www.iucnredlist.org/species/59081/78906025#habitat-ecology

  4. “Andrews Forest Map” HJ Andrews Experimental Forest Long-Term Ecological Research, 2017, https://andrewsforest.oregonstate.edu/data/map

  5. Gregory S. V. 2016. Aquatic Vertebrate Population Study in Mack Creek, Andrews Experimental Forest, 1987 to present. Environmental Data Initiative. https://doi.org/10.6073/pasta/5de64af9c11579266ef20da2ff32f702. Dataset accessed 12/01/2019.